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The championship leader had failed to score in Saturday's first part of the double-header on the Brooklyn street circuit but made sure of the necessary points to end season five on top again.
His DS Techeetah outfit took the team's title, ahead of Audi Sport ABT.
Vergne had been 22 points clear of Audi's Brazilian Lucas Di Grassi going into the final race and 25 ahead of Jaguar's New Zealander Mitch Evans.
Sebastien Buemi, winner of Saturday's eventful race from pole position for Nissan to take his first victory in more than two years, had also been in mathematical contention 26 points behind Vergne.
Di Grassi and Evans, needing to win, crashed together on the final lap while Switzerland's Buemi was third to finish as overall runner-up.
Dutch driver Robin Frijns won the final race for Virgin Racing, ahead of Britain's Alexander Sims for Andretti Autosport.
Vergne ended up with 136 points to Buemi's 119. (Reporting by Alan Baldwin in Silverstone, editing by Clare Fallon)
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